Table 1.
Parameters Used in the Application of Oncogenic Pathway Signatures to the Human Melanoma Samples
| Signature | AKT | βCAT | EGFR | ER | E2F1 | E2F3 | HER2 | MYC | p53 | p63 | PI3K | PR | RAS | SRC | STAT3 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of genes | 250 | 85 | 500 | 125 | 150 | 350 | 250 | 500 | 250 | 75 | 250 | 250 | 350 | 85 | 125 |
| No. of metagenes | 3 | 2 | 2 | 2 | 2 | 2 | 3 | 2 | 3 | 3 | 2 | 3 | 2 | 3 | 3 |
| Burn-in | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 | 1000 |
| Iterations | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 |
| Skips | 1 | 1 | 1 | 1 | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| CI | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% | 95% |
| RMA or MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 | MAS5.0 |
| Quantile normalized | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Shift scale | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Binreg Ver | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
CAT, catenin; EGFR, epidermal growth factor receptor; ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; PI3K, phosphatidylinositol 3-kinase; PR, progesterone receptor.